Inhibition of BRD Proteins Suppresses the Phenotype of Uterine Fibroids

Abstract

In aspects, the present disclosure provides a method of treating or preventing a uterine fibroid in a female mammal, the method comprising, consisting essentially of, or consisting of administering to the female mammal an effective amount of an inhibitor of bromodomain (BRD) protein.

Description

CROSS-REFERENCE TO RELATED APPLICATION

This patent application claims the benefit of U.S. Provisional Patent Application No. 63/256,855, filed Oct. 18, 2021, which is incorporated by reference herein in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with Government support under Grant Numbers HD106285 awarded by the National Institutes of Health. The Government has certain rights in this invention.

BACKGROUND

Uterine fibroids (UFs) are benign smooth muscle tumors that are a major cause of gynecologic dysfunction, such as menometrorrhagia and anemia, pelvic pressure and bulk symptoms, infertility, recurrent miscarriage, and preterm labor. UFs are the most common pelvic tumor, occurring in 80% of women. Uterine fibroids exhibit an extraordinary range of clinical presentations with lesions that routinely range from 5 mm to over 25 cm in size.

There is an ongoing need in the art to treat UFs.

BRIEF SUMMARY

In aspects, the present disclosure provides a method of treating or preventing a uterine fibroid in a female mammal, the method comprising, consisting essentially of, or consisting of administering to the female mammal an effective amount of an inhibitor of bromodomain (BRD) protein.

Additional aspects of the present disclosure are as described herein.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a diagram that illustrates bromodomain (BRD) proteins in gene regulation.

FIG. 2 is a diagram that illustrates the N6-methyladenosine (m6A) pathway in the epitranscriptome.

FIGS. 3A-3C are a Western blot image of BRD2, BRD3, BRD9, and β actin levels in UFs and myometrium from uterus (MyoF) of humans (FIGS. 3A-B) and an immunoblot analysis dot graph of the fold change in UF over MyoF of BRD2, BRD3, and BRD9 levels (FIG. 2B). P indicates the patient (n=7), M indicates the MyoF tissue (n=7), F indicates the UFs (n=22).

FIGS. 4A-4G are illustrations of the chemical structure of the BRD inhibitors TP-472 (FIG. 4A), I-BRD9 (FIG. 4B), I-BET762 (FIG. 4C), (+)-JQ1 (FIG. 4D), PFI 1 (FIG. 4E), CPI 203 (FIG. 4F), and STM2457 (FIG. 4G).

FIGS. 5A-5F are cell proliferation assay bar graphs showing the percent of relative proliferation in an immortalized human leiomyoma cell line (HuLM) and immortalized human uterine smooth muscle cell line (UTSM) that have been cultured for 24 or 48 hours in the presence or absence of the BRD inhibitors: TP-472 (FIG. 5A), OF-1 (FIG. 5B), LP99 (FIG. 5C), I-BRD9 (FIG. 5D), NVS-CECR2-1 (FIG. 5E), and BAZ2-ICR(FIG. 5F). NS, *, **, and ***indicate, not significant, p<0.05, <0.01, and <0.001 respectively.

FIGS. 6A-6F are Western blot images of proliferating cell nuclear antigen (PCNA) and β actin levels in HuLM cells treated with 0-25 μM of I-BRD9 (FIG. 6A) or TP-472 (FIG. 6B) for 48 hours, Western blot images of fibronectin (FN) and β actin levels in HuLM cells treated with 0-25 μM of I-BRD9 (FIG. 6C) or TP-472 (FIG. 6D) for 48 hours, a Western blot image of the anti-apoptosis protein Bcl-2 and β actin levels in HuLM cells treated with 0-25 μM of I-BRD9 (FIG. 6E) for 48 hours, and a micrograph of HuLM cells treated with vehicle, I-bRD9, or TP-472 for 48 hours (FIG. 6F).

FIGS. 7A-7B are cell proliferation assay scatter plot graphs showing the relative cell number of HuLM (square) and UTSM (circle) cells after treatment with 0-25 μM of I-BET762 (FIG. 7A) or (+)-JQ1 (FIG. 7B) for 48 hours.

FIGS. 8A-8B are a Western blot image of YT521-B homology domain containing protein 1 (YTHDC1), of YT521-B homology domain containing protein 2 (YTHDC2), YT521-B homology domain N6-methyladenosine RNA binding protein 2 (YTHDF2), and β actin levels in HuLM cells treated with 0-25 μM of I-BRD9 (FIG. 8A) and a Western blot image of YTHDC1, YTHDC2, methyltransferase-like protein 3 (METTL3), and β actin levels in HuLM cells treated with 0-25 μM of TP-472 (FIG. 8B) for 48 hours.

FIGS. 9A-9D are dot plot graphs of RNA-sequencing analysis showing gene groups that are upregulated (FIG. 9A) and downregulated (FIG. 9B) in HuLM cells cultured in the presence or absence of I-BRD9 and dot plot graphs of RNA-sequencing analysis showing gene groups that are upregulated (FIG. 9C) and downregulated (FIG. 9D) in HuLM cells cultured in the presence or absence of TP-472. GO: gene ontology, BP: biological process, CC: cellular component, MF: molecular function, CORUM: comprehensive resource of mammalian protein complexes, HPA: human protein atlas, HP: human phenotype ontology, WP: wikipathway.

FIGS. 10A-10B are Venn diagrams of the upregulated genes in HuLM cells treated with I-BRD9 and TP-472 (FIG. 10A) and of the downregulated genes in HuLM cells treated with I-BRD9 and TP-472 (FIG. 10B).

DETAILED DESCRIPTION

In aspects, the present disclosure provides a method of treating or preventing a uterine fibroid in a female mammal, the method comprising, consisting essentially of, or consisting of administering to the female mammal an effective amount of an inhibitor of bromodomain (BRD) protein. In aspects the female mammal is a human.

As used herein, a “uterine fibroid” (UF), is a benign tumor of the uterus that consists of a mass or population of smooth muscle cells and connective tissue that grows, usually slowly, within the uterine wall. Epidemiologic studies demonstrate that UFs, also known as leiomyomas, initially form after menarche. It is suspected that fibroid growth is due to a monoclonal, deregulated proliferation of uterine smooth muscle myometrial cells. The primary tumor cell type resulting from the growth of the fibroid are derived from myometrial cells.

UFs have a high accumulative incidence. UFs are one of the most common tumors. Complications arising from uterine fibroids account for approximately a third of all hysterectomies performed in the U.S., and are associated with high morbidity from uterine bleeding and pain. By age 50 approximately 75% of women have developed UFs. A significant number of those with UFs suffer from debilitating pelvic pain, heavy and prolonged bleeding, which may lead to anemia and iron deficiency, bowel and bladder dysfunction, and infertility. UFs also cause symptoms such as low back pain, urinary frequency and urgency, pain during intercourse (dyspareunia), can cause pre-term labor, and have a negative impact on fertility (due to cavity distension, and alteration of endometrial receptivity and sexual function).

The terms “treat,” “treating,” “treatment,” “therapeutically effective,” etc. used herein do not necessarily imply 100% or complete treatment, etc. Rather, there are varying degrees, which one of ordinary skill in the art recognizes as having a potential benefit or therapeutic effect. In this respect, the inhibitor of BRD and methods can provide any amount of any level of treatment. Furthermore, the treatment provided by the disclosed method can include the treatment of one or more conditions or symptoms of the disease or condition being treated.

The disclosed methods comprise using an effective amount of an inhibitor of BRD. An “effective amount” means an amount sufficient to show a meaningful benefit. A meaningful benefit includes, for example, detectably treating, relieving, or lessening one or more symptoms of UFs; inhibiting, arresting development, preventing, or halting further development of UFs; reducing the size and/or mass of UFs; reducing the severity of UFs; preventing UFs from occurring in a subject at risk thereof but yet to be diagnosed. The meaningful benefit observed can be to any suitable degree (10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more). In aspects, one or more symptoms are prevented, reduced, halted, or eliminated subsequent to administration of an inhibitor of BRD as described herein, thereby effectively treating the disease to at least some degree.

One skilled in the art will recognize that dosage will depend upon a variety of factors, including the age, condition or disease state, predisposition to disease, genetic defect or defects, and body weight of the subject. The size of the dose will also be determined by the route, timing and frequency of administration as well as the existence, nature, and extent of any adverse side-effects that might accompany the administration of a particular active agent and the desired effect. It will be appreciated by one of skill in the art that various conditions or disease states may require prolonged treatment involving multiple administrations.

The amount (e.g., therapeutically effective amount) of an inhibitor of BRD suitable for administration depends on, e.g., the particular route of administration and the weight of the mammal to be treated. Several doses can be provided over a period of days or weeks.

The mammal may be any suitable mammal. Mammals include, but are not limited to, the order Rodentia, such as mice, and the order Lagomorpha, such as rabbits. The mammal can be from the order Carnivora, including Felines (cats) and Canines (dogs). The mammal can be from the order Artiodactyla, including Bovines (cows) and Swines (pigs) or of the order Perissodactyla, including Equines (horses). The mammal can be of the order Primates, Cebids, or Simioids (monkeys) or of the order Anthropoids (humans and apes). In aspects, the mammal is human.

In aspects the method of treating a uterine fibroid in a female mammal, including humans, comprises administering an effective amount of TP-472. The amount (e.g., therapeutically effective amount) of TP-472 suitable for administration depends on, e.g., the particular route of administration and the weight of the mammal to be treated. Several doses can be provided over a period of days or weeks.

In aspects, the method of treating a uterine fibroid in a female mammal, including humans, comprises administering an effective amount of I-BRD9. The amount (e.g., therapeutically effective amount) of I-BRD9 suitable for administration depends on, e.g., the particular route of administration and the weight of the mammal to be treated. Several doses can be provided over a period of days or weeks.

In aspects the method of treating a uterine fibroid in a female mammal, including humans, comprises administering an effective amount of JQ1. The amount (e.g., therapeutically effective amount) of JQ1 suitable for administration depends on, e.g., the particular route of administration and the weight of the mammal to be treated. Several doses can be provided over a period of days or weeks.

In aspects the method of treating a uterine fibroid in a female mammal, including humans, comprises administering an effective amount of I-BET762. The amount (e.g., therapeutically effective amount) of I-BET762 suitable for administration depends on, e.g., the particular route of administration and the weight of the mammal to be treated. Several doses can be provided over a period of days or weeks.

Bromodomain containing (BRD) proteins are involved in many biological processes, most notably epigenetic regulation of transcription, and BRD protein dysfunction has been linked to many diseases including tumorigenesis. BRD proteins have been split into the bromodomain proteins and bromodomain and extraterminal (BET) proteins. The bromodomain, acting as the “readers” of lysine acetylation, is responsible for transducing the signal carried by acetylated lysine residues and translating it into various normal phenotype.

The epitranscriptome includes all the biochemical modifications of the RNA within a cell. Among these post-transcriptional RNA modifications, m6A is the abundant, dynamic, and reversible modification involved in many biological events and diseases. FIG. 2 summarizes some of the roles of m6A regulators in the epitranscriptome.

As used herein, the term “m6A regulator” is any molecule that regulates m6A modifications to RNA. Without wishing to be bound by theory, m6A regulators can be further categorized as “erasers,” “readers,” and “writers.” As used herein, an “eraser” is defined as a category of enzymes that demethylate m6A. m6A erasers include fat mass and obesity-associated protein (FTO) and human AlkB homolog 5 (ALKBHS). As used herein, a “reader” is defined as a protein that recognizes and binds to m6A. m6A readers include YT521-B homology domain containing proteins (YTHDC) such as YTHDC1 and YTHDC2, YT521-B homology domain N6-methyladenosine RNA binding proteins (YTHDF) such as YTHDF1, YTHDF2, and YTHDF3, eukaryotic initiation factor 3 (eIF3), fragile X messenger riboprotein 1 (FMR1), heterogeneous nuclear ribonucleoproteins (HNRNPs) such as HNRNPC, HNRNPG, and HNRNPA2B1, and insulin-like growth factor 2 mRNA-binding proteins (IGF2BP) such as IGF2BP1, IGF2BP2, and IGF2BP3. As used herein, a “writer” is defined as an m6A methyltransferase complex that post-transcriptionally adds the m6A mark. The m6A methyltransferase complex includes core subunits such as methyltransferase-like 3 (METTL3), which catalyzes the methyl transfer, and methyltransferase-like 14 (METTL14), which also methylates adenosine residues at the N(6) position of some mRNAs. The m6A methyltransferase complex also includes adaptor subunits such as RNA binding motif protein 15 (RBM15), Wilms' tumor 1-associating protein (WTAP), vir-like m6A methyltransferase associated (VIRMA), E3 ubiquitin-protein ligase Hakai (HAKAI), also known as, casitas B-lineage lymphoma-transforming sequence-like protein 1 (CBLL1), and zinc finger CCCH-type containing protein 13 (ZC3H13). These adaptors play an important role in targeting the “writers” to distinct sets of genes in the chromatin, resulting in transcript-specific m6A methylation.

BRD proteins can have a wide variety of functions via multiple gene regulation mechanisms including chromatin remodeling, modifications of histones, histone recognition and scaffolding, and various activities in transcriptional co-regulation, as shown in FIG. 1. BRD proteins are involved in many diseases, including inflammation, metabolic diseases, multiple sclerosis, cardiovascular disease, and tumorigenesis. Several small molecular inhibitors of BRD proteins have previously been developed.

TP-472, I-BRD9, (+)-JQ1, and I-BET762 are BRD inhibitors. As used herein, a “BRD inhibitor” is any agent that inhibits a BRD protein, e.g., by inhibiting the expression or function of a BRD protein. Examples of BRD inhibitors include TP-472, BAY-299, PFI-1, (+)-JQ1, bromosporine, GSK2801, OF-1, BAZ2-ICR, LP99, NI-57, PFI-4, I-BRD9, I-BET672, BI-9564, and NVS-CECR2-1.

The following includes certain aspects of the disclosure.

1. A method of treating or preventing a uterine fibroid in a female mammal, the method comprising administering to the female mammal an effective amount of an inhibitor of bromodomain protein (BRD).

2. The method of aspect 1, wherein the inhibitor of BRD is TP-472, I-BRD9, JQ1, or I-BET762.

3. The method of aspect 2, wherein the inhibitor of BRD is TP-472.

4. The method of aspect 1, wherein the female mammal is a human.

5. The method of aspect 2, wherein the female mammal is a human.

6. The method of aspect 3, wherein the female mammal is a human.

It shall be noted that the preceding are merely examples of aspects of the disclosure. Other exemplary aspects are apparent from the entirety of the description herein. It will also be understood by one of ordinary skill in the art that each of these aspects may be used in various combinations with the other aspects provided herein.

The following examples further illustrate aspects of the disclosure, but, of course, should not be construed as in any way limiting its scope.

Example

This example demonstrates dysregulation of BRD proteins in human UFs compared to myometrium and demonstrates inhibition of BRD9.

Materials and Methods

UF Tissue Sample Collection

The UF tissues were obtained from the University of Chicago Tissue Bank.

Approval from the Institutional Review Board (#20-1414) at the University of Chicago was obtained for the retrospective chart review of UF patients. Informed consent was obtained from all the patients participating in the study before surgery. The cases with an initial diagnosis of UF at University of Chicago Hospital were reviewed, and the diagnosis was confirmed by H&E evaluation and immunohistochemistry. A total of nine cases with UFs were used and human UFs (n=22) and matched myometrium tissue (n=7) were collected at the time of the hysterectomy.

Western Immunoblot

Cells were collected and lysed in RIPA lysis buffer with protease and phosphatase inhibitor cocktail (Thermo Scientific, Waltham, Mass., USA), and the protein was quantified using the Bradford method (Bio-Rad Protein Assay kit). The antibodies used were: METTL3 (ab195352, Abcam), YTHDC1 (ab122340, Abcam), YTHDC2 (35440, Cell Signaling), YTHDF2 (ab220163, Abcam), BCL-2 (ab182858, Abcam), FN (26836, Cell Signaling), PCNA (GTX100539, Genetex), BRD2 (5848, cell signaling), BRD3 (ab50818, Abcam), BRD9 (58906, Cell Signaling). The antigen-antibody complex was detected with Trident Femto Western HRP substrate (GeneTex, Irvine, Calif., USA). Specific protein bands were visualized using ChemiDoc XRS p molecular imager (Bio-Rad, Hercules, Calif., USA).

Cell Culture

The immortalized human leiomyoma cell line (HuLM) and immortalized human uterine smooth muscle (UTSM) cells were cultured and maintained in phenol red-free, Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12. The cells were grown at 37° C. and 5% CO₂ in an incubator with saturating humidity.

BRD Inhibitor Screening by MTT Assay

Cell proliferation was measured using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. 2×10⁴UTSM or HuLM cells per well were seeded into 12-well tissue culture plates in the absence or presence of each BRD inhibitor from Table 1 for 24 hours or 48 hours. The inhibitors used in this assay were from the Epigenetic Library at the University of Illinois at Chicago. This assay was performed three times in triplicate.

	TABLE 1
	BRD Inhibitor	Target	Notes
	TP-472	BRD9/7	bromodomain
	BAY-299	BRD1, TAF1	bromodomain
	PFI-1	BET family	bromodomain
	(+)-JQ1	BET family	bromodomain
	bromosporine	broad spectrum	bromodomain
		bromodomain
	GSK2801	BAZ2A/2B	bromodomain, zn finger
	OF-1	BRPF1B/2/3	chromatin regulator
			(PHD, bromodomains)
	BAZ2-ICR	BAZ2A/2B	bromodomain, zn finger
	LP99	BRD9/7	bromodomain
	NI-57	BRPF1B/2/3	chromatin regulator
			(PHD, bromodomains)
	PFI-4	BRPF1B	chromatin regulator
			(PHD, bromodomains)
	I-BRD9	BRD9	bromodomain
	BI-9564	BRD9/7	bromodomain
	NVS-CECR2-1	CECR2	chromatin remodeling
			(bromodomain)

BRD Inhibition Treatments

HuLM cells were cultured in phenol red-free, 10% fetal bovine serum Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12 at 37° C., 5% CO₂ in the absence or presence of the BRD inhibitors I-BRD9 and TP-472 for 48 hours respectively. The concentrations of both inhibitors were used in the range of 0-25 μM. Cells were collected after treatment for Western immunoblot as described above.

Microscopy

HuLM cells were imaged using (microscope and imaging software).

Cell Proliferation Assay of BRD Inhibition

Cell proliferation was measured using trypan blue exclusion assay. UTSM and HuLM cells (2×10⁴ cells per well) were seeded into 12-well tissue culture plates. After 24 hours the cells were cultured in the absence or presence of the BRD inhibitor I-BET762 or (+)-JQ1 at a dose range from 1-25 μM for 48 hours. DMSO was used as a vehicle control. Cells were trypsinized, collected by centrifuge, and resuspended in serum-free medium. Equal volumes of 0.4% trypan blue and cell suspension were mixed and cells were counted using a hemacytometer.

Statistical Analysis of Immunoblots and Proliferation Assays

Comparisons between groups were made using student t-tests. In figures, NS, *,**, and ***indicate, not significant, p<0.05, <0.01, and <0.001 respectively.

RNA-Sequencing

To determine the mechanism underlying the inhibitory effect of BRD9 inhibition on the UFs, the HuLM cells were treated with BRD9 inhibitor I-BRD9 (5 μM, n=4), TP-472 (5 μM, n=3), and DMSO vehicle control (n=4) for 48 hr. RNA was isolated using Trizol. RNA quality and quantity were assessed using the Agilent bio-analyzer. Strand-specific RNA-SEQ libraries were prepared using a TruSEQ total RNA-SEQ library protocol (Illumina provided). Library quality and quantity were assessed using the Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ6000 (illumine provided reagents and protocols).

Transcriptome Data Analysis

A variety of R packages was used for this analysis. All graphics and data wrangling were handled using the tidyverse suite of packages (available from tidyverse.org). All packages used are available from the Comprehensive R Archive Network (CRAN), Bioconductor.org, or GitHub. The reads were mapped to the human reference transcriptome using STAR, version 2.6.1d, as previously described (Dobin et al., Bioinformatics 29 (1):15-21 (2013)). The quality of raw reads, as well as the results of STAR mapping, are generated using fastqc (available from bioinformatics.babraham.ac.uk/projects/fastqc/) and multiqc (available from multiqc.info). Raw reads were mapped to the human reference transcriptome using Salmon, version 1.4.0 (available from combine-lab.github.io/salmon/). After reading mapping with Salmon, Bioconductor (available from bioconductor.org/packages/release/bioc/html/tximport) was used to read Salmon outputs into the R environment. Annotation data from Gencode V34 was used to summarize data from transcript-level to gene-level.

Results

BRD Protein Expression in Human UF Cells

Human UFs (n=22) and matched MyoF tissue (n=7) were collected at the time of hysterectomy from seven patients. Immunoblot analysis was performed on human uterine fibroids (n=22) and matching myometrium tissue (n=7) to determine the levels of the BRD proteins, BRD2, BRD3, and BRD9 (FIGS. 3A-B). The protein levels of BRD2 and BRD9, but not BRD3, were significantly upregulated in UFs compared to matched myometrium tissues (FIG. 3C). Among 22 UFs analyzed, 96% (21/22, p<0.01), 55% (12/22), 82% (18/22, p<0.01) exhibited the upregulation of BRD2, BRD3, and BRD9 respectively, suggesting that aberrant BRD protein expression may contribute to the pathogenesis of UFs.

Screening of BRD Inhibitors in UF Cells

To examine the biological impact of BRD inhibition on the UFs, 14 BRD inhibitors, listed in Table 1 and select structures shown in FIGS. 4A-D, were screened to identify specific and potent BRD inhibitors in UF cells. Cell proliferation was measured in immortalized uterine smooth muscle (UTSM) and immortalized human uterine leiomyoma (HuLM) cells in the presence or absence of each BRD inhibitor for 24 hours and 48 hours respectively. 43% of these BRD inhibitors, TP-472 (FIG. 5A), OF-1 (FIG. 5B), LP99 (FIG. 5C), I-BRD9 (FIG. 5D), NVS-CECR2-1 (FIG. 5E), and BAZ2-ICR(FIG. 5F), selectively inhibited UF, but not myometrial cell proliferation.

Inhibiting BRD9 Suppresses the Phenotype of UF Cells

To examine how BRD inhibition affects UF cell phenotypes HuLM cells were cultured in the absence or presence of the BRD inhibitors I-BRD9 and TP-472. After treatment the cells underwent immunoblotting for proliferating cell nuclear antigen (PCNA) (FIGS. 6A-B) and fibronectin (FN) (FIG. 6C-D). Both I-BRD9 and TP-472 exhibited anti-uterine fibroid cell proliferation demonstrated by decreasing the levels of PCNA, a marker for cell proliferation. Both I-BRD9 and TP-472 also decreased FN levels. Additionally, I-BRD9 increased the expression of the anti-apoptosis protein BCL-2 (FIG. 6E). BRD9 inhibition also resulted in morphological changes to the HuLM cells as shown in (FIG. 6F). To further investigate the effects of BRD inhibition on cell proliferation UTSM and HuLM cells were in the absence or presence of the BRD inhibitors I-BET762 (FIG. 7A) and (+)-JQ1 (FIG. 7B). Both I-BET762 and (+)-JQ1 reduced cellular proliferation more potently in UF cells than myometrium cells in a dose dependent manner.

Inhibiting BRD9 Modulates the Levels of m6A Regulators in UF Cells

To investigate the role of BRD9 in m6A regulator levels in UF cells, HuLM cells were cultured in the absence or presence of the BRD inhibitors I-BRD9 and TP-472. After the treatment, the cells underwent immunoblot analysis for the m6Aregulators YTHDC1, YTHDC2, YTHDF2, and METTL3. The inhibition of BRD9 with I-BRD9 demonstrates a dose-dependent downregulation of expression of YTHDC1, YTHDC2, and YTHDF2 (FIG. 8A). The inhibition of BRD9 with TP-472 demonstrates a dose-dependent downregulation of expression of YTHDC1, YTHDC2, and METTL3 (FIG. 8B). The inhibition of BRD proteins with I-BRD9 and TP-472 downregulating the expression of METTL3, YTHDC1, YTHDC2, and YTHDF2, which are the key regulators for m6A modification, indicates the tight link between BRD proteins and the epitranscriptomic landscape.

Inhibiting BRD9 Alters Pathways Related to Biological Processes and Transcription Factors in UF Cells

To investigate the role of BRD9 in pathways related to biological processes and transcription factors HuLM cells were cultured in the absence or presence of the BRD inhibitors I-BRD9 or TP-472. After the treatment, RNA sequence analysis was performed. Transcriptome analysis reveals a distinct pattern between BRD9 inhibitors and control groups in uterine fibroid cells. Bioinformatic analysis showed that both IBRD9 (FIGS. 9A-B) and TP472 (FIGS. 9C-D) altered the pathways related to biological processes, transcriptional factors, etc.

Further analysis was performed to identify differentially expressed genes (DEGs) between the I-BRD9 and TP-472 treatment groups (Table 2). VOOM analysis showed that I-BRD9 and TP-472 shared 852 up-regulated genes (FIG. 10A) and 610 downregulated genes (FIG. 10B). Hallmark analysis reveals a commonly distinct pathway alteration in response to inhibition of BRD by both TP472 and IBRD9, such as E2F, MYC Target, G2M checkpoint, and mitotic spindle pathways.

TABLE 2
Table of Differentially Expressed Genes (DEGs)
	IBRD9 vs Control	TP472 vs Control
	Downregulated	1098	975
	Not Significant	9788	9839
	Upregulated	1274	1346

All references, including publications, patent applications, and patents, cited herein are hereby incorporated by reference to the same extent as if each reference were individually and specifically indicated to be incorporated by reference and were set forth in its entirety herein.

The use of the terms “a” and “an” and “the” and “at least one” and similar referents in the context of describing the invention (especially in the context of the following claims) are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context. The use of the term “at least one” followed by a list of one or more items (for example, “at least one of A and B”) is to be construed to mean one item selected from the listed items (A or B) or any combination of two or more of the listed items (A and B), unless otherwise indicated herein or clearly contradicted by context. The terms “comprising,” “having,” “including,” and “containing” are to be construed as open-ended terms (i.e., meaning “including, but not limited to,”) unless otherwise noted. Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., “such as”) provided herein, is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention unless otherwise claimed. No language in the specification should be construed as indicating any non-claimed element as essential to the practice of the invention.

Preferred aspects of this invention are described herein, including the best mode known to the inventors for carrying out the invention. Variations of those preferred aspects may become apparent to those of ordinary skill in the art upon reading the foregoing description. The inventors expect skilled artisans to employ such variations as appropriate, and the inventors intend for the invention to be practiced otherwise than as specifically described herein. Accordingly, this invention includes all modifications and equivalents of the subject matter recited in the claims appended hereto as permitted by applicable law. Moreover, any combination of the above-described elements in all possible variations thereof is encompassed by the invention unless otherwise indicated herein or otherwise clearly contradicted by context.

Claims

1. A method of treating or preventing a uterine fibroid in a female mammal, the method comprising administering to the female mammal an effective amount of an inhibitor of bromodomain protein (BRD).

2. The method of claim 1, wherein the inhibitor of BRD is TP-472, I-BRD9, JQ1, or I-BET762.

3. The method of claim 2, wherein the inhibitor of BRD is TP-472.

4. The method of claim 1, wherein the female mammal is a human.

5. The method of claim 2, wherein the female mammal is a human.

6. The method of claim 3, wherein the female mammal is a human.